Molcontroller

Molcontroller provides molecular manipulation functions within Visual Molecular Dynamics (VMD) to perform translations and rotations of selected molecules or molecular components for modeling and simulation setup.

Key Features:

• Molecular translation and rotation: Performs translations and rotations of whole molecules or selected molecular components within VMD.
• Selection-based operations: Applies manipulations to user-selected molecules or specific parts of molecules.
• Tcl/Tk implementation: Implemented using the Tcl/Tk toolkit and interfaces with VMD's Tcl scripting environment.
• Tcl script automation: Executes Tcl commands to carry out manipulations that would otherwise require manual Tcl scripting.

Scientific Applications:

• Model preparation for molecular dynamics: Adjusts coordinates and orientations of molecules during setup for molecular dynamics simulations in VMD.
• Theoretical simulation support: Performs coordinate manipulations required in theoretical simulation studies.
• Structural modeling workflows: Enables positional and orientational adjustments of molecular components during modeling tasks and workflows.

Methodology:

Implemented in Tcl/Tk and integrated with VMD, Molcontroller performs translations and rotations by generating and executing Tcl commands on selected molecules or molecular components within the VMD environment.